Background: Starting 2020, the medical guidelines were shacked by COVID-19 pandemic. The threshold for hospital admission increased in order to limit Severe Acute Respiratory Syndrome coronavirus 2 spread. All this affected screening such as for lung cancer which remained largely undiagnosed. On the other hand, it became challenging to differentiate easily between COVID-19 and other diseases such as atypical infections and simple community acquired pneumonia. Moreover, immunocompromised patients are at higher risk of COVID-19 infection overshadowing any other infection such as tuberculosis and non-tuberculosis infections. Case Presentation: We present the case of an 85-year-old female with a long history of scleroderma treated with methotrexate. Patient had non-resolving pneumonia and after two negative RT-PCR, bronchoalveolar lavage showed positive Real Time Polymerase Chain Reaction. Imaging showed persistent 2.6 cm solid nodule in left upper lobe worrisome for an underlying neoplasm. However, culture of Bronchoalveolar lavage grew with few colonies of acid fast bacilli making the diagnosis atypical mycobacteria highly probable especially that patient is chronically immunosuppressed. Unfortunately, she refused further genotyping. Conclusion: To authors’ knowledge that are no, or few reported cases of associated COVID-19 with atypical mycobacterial infections and the treatment modalities are unclear. The diagnosis of mycobacterial infections is usually difficult and in the setting of COVID-19 this becomes more challenging. Hence, a more thorough clinical approach is needed for the future to help clinicians diagnose and treat complicated cases of COVID-19 and concomitant other infections such as TB or Nontuberculous Mycobacteria. Furthermore, amidst the pandemic screening of lung cancer should continue while maintaining safety precautions.

Keywords: Covid-19, screening lung cancer, atypical mycobacteria, NTM, pneumonia, methotrexate, scleroderma, case report, TB